ToPS: ReverseComplementDNA.hpp Source File

00001 /*
00002  *       ReverseComplementDNA.hpp
00003  *
00004  *       Copyright 2011 Andre Yoshiaki Kashiwabara <akashiwabara@usp.br>
00005  *                      �gor Bon�dio <ibonadio@ime.usp.br>
00006  *                      Vitor Onuchic <vitoronuchic@gmail.com>
00007  *                      Alan Mitchell Durham <aland@usp.br>
00008  *
00009  *       This program is free software; you can redistribute it and/or modify
00010  *       it under the terms of the GNU  General Public License as published by
00011  *       the Free Software Foundation; either version 3 of the License, or
00012  *       (at your option) any later version.
00013  *
00014  *       This program is distributed in the hope that it will be useful,
00015  *       but WITHOUT ANY WARRANTY; without even the implied warranty of
00016  *       MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
00017  *       GNU General Public License for more details.
00018  *
00019  *       You should have received a copy of the GNU General Public License
00020  *       along with this program; if not, write to the Free Software
00021  *       Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
00022  *       MA 02110-1301, USA.
00023  */
00024 
00025 #ifndef REVERSE_COMPLEMENT_HPP
00026 #define REVERSE_COMPLEMENT_HPP
00027 
00028 #include "crossplatform.hpp"
00029 
00030 #include "ProbabilisticModelDecorator.hpp"
00031 #include "DiscreteIIDModel.hpp"
00032 #include "Symbol.hpp"
00033 namespace tops {
00034 
00035   class DLLEXPORT ReverseComplementDNA : public ProbabilisticModelDecorator {
00036   private:
00037     AlphabetPtr revAlphabet;
00038     int _seqLength;
00039     void revcomp(Sequence & revCompSeq, const Sequence & s, int begin,  int end) const;
00040   public:
00041     ReverseComplementDNA(ProbabilisticModelPtr m) : ProbabilisticModelDecorator(m)
00042     {
00043       revAlphabet =  AlphabetPtr(new Alphabet());
00044       AlphabetPtr a = m->alphabet();
00045       std::string A("A");
00046       std::string C("C");
00047       std::string G("G");
00048       std::string T("T");
00049       for(int i = 0; i < (int)a->size(); i++){
00050         SymbolPtr s = a->getSymbol(i);
00051         if(s->name() == A) {
00052           revAlphabet->createSymbol(T);
00053         } else if (s->name() == G) {
00054           revAlphabet->createSymbol(C);
00055         } else if (s->name() == C) {
00056           revAlphabet->createSymbol(G);
00057         } else if (s->name() == T) {
00058           revAlphabet->createSymbol(A);
00059         }
00060       }
00061     };
00062     virtual ~ReverseComplementDNA(){};
00063     virtual double evaluate(const Sequence & s, unsigned int begin, unsigned int end) const;
00064     virtual Sequence & choose(Sequence & h, int size) const ;
00065     virtual Sequence & choose(Sequence &h, int initial_phase, int size) const;
00066     virtual double prefix_sum_array_compute(int begin , int end) ;
00067     virtual double prefix_sum_array_compute(int begin , int end, int phase);
00068     virtual bool initialize_prefix_sum_array(const Sequence & s, int phase);
00069     virtual bool initialize_prefix_sum_array(const Sequence & s) ;
00070     virtual std::string str() const;
00071     std::string model_name () const;
00072     virtual ProbabilisticModelParameters parameters() const ;
00073     virtual void initialize(const ProbabilisticModelParameters & p) ;
00074 
00075   };
00076   typedef boost::shared_ptr<ReverseComplementDNA> ReverseComplementDNAPtr;
00077 }
00078 
00079 #endif